Sometimes when I do a sift analysis, I noticed that the input and output
alleles are different. I don't understand why and what does it means ?
could you explain it to me ?
For example, here you can see that the input allele is G/A for chr2
(first line) and the output is G/T
*
input file:
chr2 230341630 + G/A
chr2 43881517 + A/T
chr10 115912482 - G/T
chr10 115900918 - C/T
*
output file:
#Chrom Position Strand Allele Codons Transcript ID Protein ID
Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num
seqs at position User Comment
chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA
EXON CDS rs1803846:A Unknown Not scored NA NA NA
chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L
EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7
chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L
EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2
chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271*
EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A
Regards.
Charlotte Gueydan
--
*Charlotte Gueydan *, PhD.
INSERM/Université Pierre et Marie Curie
Hôpital Tenon - bâtiment de recherche
4, rue de la Chine
75020 Paris cedex 20
tel : 01 56 01 83 75